Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_093396418.1 BM091_RS13110 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_900114975.1:WP_093396418.1 Length = 396 Score = 357 bits (915), Expect = e-103 Identities = 192/391 (49%), Positives = 246/391 (62%), Gaps = 12/391 (3%) Query: 21 DQYVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQK 80 D + +TY R V +G GCRLWD +G Y DFVAGIA C LGH + +A+ Q +K Sbjct: 10 DSVICNTYVREEVTFVRGSGCRLWDEKGNEYRDFVAGIAVCNLGHCPENVAKAICDQARK 69 Query: 81 LHHISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQP 140 L H+SNLYY Q LA +V+ S AD+VFFCNSGAEANEAAIKL RKY+ Sbjct: 70 LVHVSNLYYTEPQVELAAELVKRSFADRVFFCNSGAEANEAAIKLARKYSRDRFGPGRFH 129 Query: 141 VILSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRR 200 VI + K+SFHGRTLAT++ATGQ K K F+PL DGF YV ++ I A+E A+TD + Sbjct: 130 VI-TMKNSFHGRTLATLSATGQEKVHKGFEPLVDGFVYVDFDSIEAVEAAVTD------K 182 Query: 201 VAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGI 260 A+M+E +QGEGGVR Y K +R +C+E +LL+ DEVQVG+GRTG + YE + Sbjct: 183 TCAVMVEPIQGEGGVRIPSPGYLKGLRELCNEKKLLLIFDEVQVGMGRTGSLFAYEQEEV 242 Query: 261 EPDIFTSAKGLAGGIPIGAMMCK-DSCAVFNPGEHASTFGGNPFSCAAALAVVETLEQEN 319 EPDI T AK LA G+P+GAM+ + D + F PG HASTFGG P AAAL V T+ Q Sbjct: 243 EPDIMTLAKALANGLPMGAMLAREDVASSFGPGSHASTFGGTPLVAAAALETVRTIAQRT 302 Query: 320 LLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGL 379 L+ V G LK L +KY + DVRG GL+ ME L++ +VK+ +EKG Sbjct: 303 FLDRVKTMGRYFLDKLKKLEQKYTFVKDVRGRGLMVAME----LDIPGAPIVKSCLEKGA 358 Query: 380 LLAPAGPKVLRFVPPLIVSAAEINEAIALLD 410 L+ K+LRF PPLIV EI+ + +LD Sbjct: 359 LINCVQEKILRFTPPLIVEREEIDWLVEILD 389 Lambda K H 0.319 0.136 0.406 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 454 Number of extensions: 16 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 418 Length of database: 396 Length adjustment: 31 Effective length of query: 387 Effective length of database: 365 Effective search space: 141255 Effective search space used: 141255 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory